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Oligonucleotide probes have long been used to detect complementary nucleic acid sequences in a nucleic acid of interest (the xe2x80x9ctargetxe2x80x9d nucleic acid). In some assay formats, the oligonucleotide probe is tethered, i.e., by covalent attachment to a solid support, and arrays of oligonucleotide probes immobilized on solid supports have been used to detect specific nucleic acid sequences in a target nucleic acid. See, e.g., published PCT Application Nos. WO 89/10977 and 89/11548.
The development of VLSIPS(trademark) technology has provided methods for making very large arrays of polymer sequences, including polypeptides and polynucleotides, on very small substrates. See U.S. Pat. No. 5,143,854 and published PCT Application Nos. WO 90/15070 and 92/10092, each of which is incorporated herein by reference in its entirety for all purposes. U.S. patent application Ser. No. 08/082,937, filed Jun. 25, 1993, now abandoned, describes methods for making arrays of oligonucleotide probes that can be used to provide the complete sequence of a target nucleic acid and to detect the presence of a nucleic acid containing a specific nucleotide sequence. Microfabricated arrays of large numbers of oligonucleotide probes, called GeneChips(copyright) microfabricated arrays, offer great promise for a wide variety of applications, e.g., sequencing-by-hybridization techniques (SBH) and diagnostic methods for detecting genetic and other disorders.
A major consideration in nucleic acid hybridization analyses using these arrays, as well as with other methods, is the rate at which that hybridization occurs. This hybridization rate can be affected by a variety of conditions, including the concentration of the target nucleic acid in the sample, the temperature of the hybridization reaction, the composition of the hybridization solution and others. In addition, hybridization reactions in oligonucleotide array formats are also affected by the level of mixing of the target nucleic acid during the hybridization. Such mixing typically results in the presentation of a maximal amount of target nucleic acid to the probes on the surface of the array.
Given the increased efficiency of VLSIPS(trademark) based hybridization analyses, it is desirable to provide integrated devices which are capable of optimizing a number of the specific conditions of these hybridization reactions. In particular, it would be desirable to provide a hybridization apparatus which is capable of delivering a sample to an array, mixing the sample during hybridization, maintaining the sample at an optimal temperature for hybridization, and removing the sample from the chamber following the hybridization. The present invention meets these and other needs.
The present invention generally provides novel apparatuses for rapidly and efficiently carrying out repeated hybridizations of a target nucleic acid to an array of nucleic acid probes. The apparatuses of the invention typically include a fluid delivery system for delivering and injecting selected fluids into an array cartridge or package which includes a hybridization chamber having a polymer array incorporated therein. Also included in some embodiments of the apparatuses of the invention is a mounting system for holding the hybridization chamber within the array cartridge in fluid communication with the fluid delivery system. The apparatuses also include a fluid mixing system for mixing the fluids within the hybridization chamber, a temperature control system for monitoring and controlling the temperature of the fluids within the hybridization chamber, and a process control system for monitoring and selectively controlling the fluid delivery system, the fluid mixing system and the temperature control system.